Benthic algae were used to identify reference conditions of springs for bioassessment purposes. Benthic algae and environmental factors were quantified in 70 springs (nonthermal and mostly near-natural) in the southeastern Alps. Spring types were identified by fuzzy clustering of nondiatom, benthic algal assemblages. Canonical Correspondence Analysis (CCA) and indicator species analysis (IndVal) were used to identify the most relevant environmental determinants of taxonomic composition in springs and to characterize the ecological traits of key taxa. A total of 120 macro- and microscopic benthic pro- and eukaryotic algae (excluding diatoms) were identified. Cyanobacteria (especially Chroococcales and Oscillatoriales) were strongly prevalent. Seven spring types were identified by fuzzy clustering of nondiatom, benthic algal assemblages. IndVal identified 22 taxa that were significant indicators of spring type, and fuzzy clustering based on environmental preferences identified 18 other important taxa associated with spring type. Spring types differed in environmental features, species richness, and diversity. Mid-to-high altitude, oligotrophic, carbonate flowing springs (rheocrenes) with medium conductivity were the most common spring type and were characterized by shade-tolerant (Chroococcales) or rheophilic (Tapinothrix varians) cyanobacteria. Low-altitude, shaded, and slightly NO₃-N-enriched carbonate rheocrenes with medium-to-high conductivity supported rheophilic or eutraphentic cyanobacteria and red algae. Siliceous rheocrenes had benthic algal assemblages dominated by soft-water, rheophilic cyanobacteria and by the rheobiontic chrysophyte, Hydrurus foetidus. Mostly siliceous seepages and pool springs supported predominantly chlorophytes, especially filamentous Zygnematales. Xerotolerant cyanobacteria were common on carbonate rock-face seepages. Tufa springs were characterized by cyanobacteria and by the desmid, Oocardium stratum. In iron springs, benthic algae (mainly filamentous green algae and xanthophytes) were poorly developed, whereas iron bacteria were common. The most influential factors were pH and conductivity, shading, NO₃-N, temperature, current velocity, and substratum particle size. The spring types identified may prove useful as references for assessments of ecological integrity naturalness value, at least for the Alps ecoregion.